1 BIOL 4475-110, 80361, Proteomics Fall 2019 Texas A&M University-Central Texas COURSE DATES, MODALITY, AND LOCATION Time/Day: Lecture: TR 9:30 am – 10:45 am Laboratory: T 11:15 am – 2:15 pm Where: Lecture: Warrior Hall 315 Laboratory: Heritage Hall 315 Office Hours: M 2:30 pm – 5:30 pm TR 8:15 am – 9:15 am By appointment: Please contact me through Canvas to set up a time in advance. Mode of instruction and course access: This course meets face-to-face, (with supplemental materials made available online). This course uses the A&M-Central Texas Canvas Learning Management System [https://tamuct.instructure.com/]. INSTRUCTOR AND CONTACT INFORMATION Instructor: Dr. Linh Pham, Assistant Professor of Chemistry Office: TAMUCT Heritage Hall, Room 302F Phone: 254-519-8012 (office) Email: Please contact me through Canvas. Student-instructor interaction In this class, face to face interaction with the instructor is one of the most effective ways to learn. Therefore; I encourage my students to go to my office hours whenever you have questions. If students cannot make it to my office hours, don’t hesitate to contact me by through Canvas for an appointment. I will reply within 24 hours, usually within couples of hours on weekdays. Response time may vary in weekends and holidays. WARRIOR SHIELD Emergency Warning System for Texas A&M University-Central Texas Warrior Shield is an emergency notification service that gives Texas A&M University-Central Texas the ability to communicate health and safety emergency information quickly via email, text message, and social media. All students are automatically enrolled in Warrior Shield through their myCT email account. Connect to Warrior Shield by 911Cellular [https://portal.publicsafetycloud.net/Account/Login] to change where you receive your alerts or to opt out. By staying enrolled in Warrior Shield, university officials can quickly pass on safety-related information, regardless of your location.
BIOL 4475-110, 80361, Proteomics Fall 2019 Texas A&M University-Central Texas
COURSE DATES, MODALITY, AND LOCATION
Time/Day: Lecture: TR 9:30 am – 10:45 am
Laboratory: T 11:15 am – 2:15 pm
Where: Lecture: Warrior Hall 315
Laboratory: Heritage Hall 315
Office Hours: M 2:30 pm – 5:30 pm
TR 8:15 am – 9:15 am
By appointment: Please contact me through Canvas to set up a time in advance.
Mode of instruction and course access:
This course meets face-to-face, (with supplemental materials made available online). This course uses the A&M-Central Texas Canvas Learning Management System [https://tamuct.instructure.com/].
INSTRUCTOR AND CONTACT INFORMATION Instructor: Dr. Linh Pham, Assistant Professor of Chemistry Office: TAMUCT Heritage Hall, Room 302F
Phone: 254-519-8012 (office)
Email: Please contact me through Canvas.
Student-instructor interaction In this class, face to face interaction with the instructor is one of the most effective ways to learn.
Therefore; I encourage my students to go to my office hours whenever you have questions. If
students cannot make it to my office hours, don’t hesitate to contact me by through Canvas for an
appointment. I will reply within 24 hours, usually within couples of hours on weekdays.
Response time may vary in weekends and holidays.
WARRIOR SHIELD Emergency Warning System for Texas A&M University-Central Texas Warrior Shield is an emergency notification service that gives Texas A&M University-Central Texas the ability to communicate health and safety emergency information quickly via email, text message, and social media. All students are automatically enrolled in Warrior Shield through their myCT email account. Connect to Warrior Shield by 911Cellular [https://portal.publicsafetycloud.net/Account/Login] to change where you receive your alerts or to opt out. By staying enrolled in Warrior Shield, university officials can quickly pass on safety-related information, regardless of your location.
COURSE INFORMATION Course Overview and description Proteomics seeks to identify and to characterize all the proteins synthesized in a cell or tissue. Based on this information, one can then try to understand how individual proteins and protein-collectives function within an organism.
CHEM 4475 focuses on the fundamental concepts of proteomics and hands-on practice of current techniques used in current proteomics. Three hours of lecture and three hours of laboratory per week.
Prerequisite: BIOL 4470, BIOL 4471
Course Objective The course will focus on current methodology used in protein analysis and identification including protein electrophoresis, chromatography, mass spectrometry, and protein database analysis. Current research advances and case studies are also examined. Student Learning Outcomes (SLOs)
Students will: 1. Understand the theory of protein analysis techniques 2. Explain the chemistry underlying the biological processes involving proteins 3. Understand the practical application of proteomic studies 4. Master basic techniques in proteomics lab and demonstrate ability to write scientific lab
Required Reading and Textbook(s) Lecture textbook: Twyman, R. 2013. Principles of Proteomics, 2nd ed. Garland Science. ISBN-
I expect you to read the corresponding chapters in your textbook before coming to class.
Assignments: There will be eight assignments of equal ten points to be turned in in class.
The assignments are due at the beginning of the next class.
Exams: Exams may be take-home or in-class, as determined by the instructor. Exams 1 &2 are non-cumulative. Final exam is cumulative. No make-up exams will be given without prior notification and approval.
Lab Reports: There will be three formal lab reports and eight lab notebook reports. Your grade will be determined primarily by the contents of the report and the accuracy of the results. However, the neatness and overall presentation of the report are also important. More details regarding the lab reports will be provided later.
Lecture attendance is important for student’s success in this course. If students miss more than three classes they will lose 20 points for attendance. No make-up of missed class is available.
Lab attendance is mandatory. A maximum of three absences will be allowed; additional absences in lab will result in an “F” for the entire course, regardless of excuse. No make-up of missed labs is available. Absence from lab includes arriving late (more than 30 minutes) or leaving before lab is dismissed.
Mandatory Laboratory Safety Training:
All students are required to take the mandatory Laboratory Safety Training Module - found in your Modules tab in CANVAS.
See “Science Policy” for more detail.
Grading Criteria Rubric and Conversion
Percentage Course Grades
90% or higher A
59.99% or lower F A 4.00 (90 +) Achievement that is outstanding relative to the level necessary to meet course
B 3.00 (80-89%) Achievement that is significantly above the level necessary to meet course
C 2.00 (70–79%) Achievement that meets the course requirements in every respect.
D 1.00 (60–69%) Achievement that is worthy of credit even though it fails to meet fully course
F 0.00 (<60%) Represents failure and signifies that the work was either (1) completed but at a
level of achievement that is not worthy of credit or (2) was not completed and there was no
agreement between the instructor and the student that the student would be awarded an “I”
I (Incomplete) The “I” shall be assigned at the discretion of the instructor when, due to
extraordinary circumstances, the student was prevented from completing the work of the course
11 (November 4) Chapter 8: Protein Modification in Proteomics Exam 2 (Chapters 5, 6, and 7)
Experiment 6A: Comparative Proteomics: Fish Protein Extraction from Muscle + Load, Run, and Stain Gels
12 (November 11) Chapter 9: Protein Microarrays Experiment 6B: Comparative Proteomics: Destain and Dry Gels + Collect Data
13 (November 18) Handout: Analysis and Interpretation of Proteomic Data
Experiment 6C: Comparative Proteomics: Analysis and Interpretation of Results
14 (November 25) Chapter 10: Application of Proteomics
15 (December 2) Recent Publications in Proteomics Lab Review
16 (December 9) Final Exam
Important University Dates
August 12, 2019 Classes Begin for Minimester
August 23, 2019 Classes End for Minimester
August 26, 2019 Classes Begin for Fall Semester
August 26, 2019 Add, Drop, and Late Registration Begins for 16- and First 8-week Classes $25 Fee assessed for late registrants
August 28, 2019 Deadline for Add, Drop, and Late Registration for 16- and First 8-week
September 2, 2019 Labor Day (University Closed)
September 3, 2019 Deadline to Drop First 8-week Classes with No Record
September 11, 2019 Deadline to drop 16-week Classes with No Record
October 1, 2019 Deadline for Teacher Education and Professional Certification Applications
October 4, 2019 Deadline to Drop First 8-week Classes with a Quit (Q) or Withdraw (W)
October 15, 2019 Deadline for Clinical Teaching/Practicum Applications
October 18, 2018 Classes End for First 8-week Session
October 18, 2019 Deadline to Withdraw from University for First 8-Week Classes (WF)
October 21, 2019 Add, Drop, and Late Registration Begins for Second 8-Week Classes $25 Fee assessed for late registrants
October 21, 2019 Classes Begin for Second 8-Week Session
October 21, 2019 Class Schedule Published for Spring Semester
October 22, 2019 Deadline for Faculty Submission of First 8-Week Class Final Grades (due by 3pm)
October 23, 2019 Deadline for Add, Drop, and Late Registration for Second 8-Week Classes
October 25, 2019 Deadline for Graduation Application for Ceremony Participation
October 28, 2019 Deadline to Drop Second 8-Week Classes with No Record
November 4, 2019 Registration Opens for Spring Semester
November 8, 2019 Deadline to Drop 16-Week Classes with a Quit (Q) or Withdraw (W)
November 11, 2019 Veteran's Day (University Closed)
November 28-29, 2019 Thanksgiving (University Closed)
November 29, 2019 Deadline to Drop Second 8-Week Classes with a Quit (Q) or Withdraw (W)
December 13, 2019 Deadline for Applications for Tuition Rebate for Fall Graduation (5pm)
December 13, 2019 Deadline for Degree Conferral Applications to the Registrar's Office $20 Late Application Fee
December 13, 2019 Deadline to Withdraw from University for 16- and Second 8-Week Classes
December 13, 2019 Fall Semester Ends
December 13, 2019 Fall Commencement Ceremony
December 17, 2019 Deadline for Faculty Submission of 16-Week and Second 8-Week Final Class Grades (due by 3pm)
December 23, 2019 - January 1, 2020
Winter Break (University Closed)
TECHNOLOGY REQUIREMENTS AND SUPPORT Technology Requirements This course will use the A&M-Central Texas Instructure Canvas learning management system. Logon to A&M-Central Texas Canvas [https://tamuct.instructure.com/] or access Canvas through the TAMUCT Online link in myCT [https://tamuct.onecampus.com/]. You will log in through our Microsoft portal.
Username: Your MyCT email address. Password: Your MyCT password Canvas Support Use the Canvas Help link, located at the bottom of the left-hand menu, for issues with Canvas. You can select “Chat with Canvas Support,” submit a support request through “Report a Problem,” or call the Canvas support line: 1-844-757-0953. For issues related to course content and requirements, contact your instructor. Other Technology Support For log-in problems, students should contact Help Desk Central 24 hours a day, 7 days a week
Email: helpdes[email protected] Phone: (254) 519-5466 Web Chat: [http://hdc.tamu.edu]
Please let the support technician know you are an A&M-Central Texas student.
UNIVERSITY RESOURCES, PROCEDURES, AND GUIDELINES Drop Policy If you discover that you need to drop this class, you must complete a Drop Request Form [https://www.tamuct.edu/registrar/docs/Drop_Request_Form.pdf]. Professors cannot drop students; this is always the responsibility of the student. The Registrar’s Office will provide a deadline on the Academic Calendar for which the form must be completed, signed and returned. Once you return the signed form to the Registrar’s Office, you must go into Warrior Web and confirm that you are no longer enrolled. If you still show as enrolled, FOLLOW-UP with the Registrar’s Office immediately. You are to attend class until the procedure is complete to avoid penalty for absence. Should you miss the drop deadline or fail to follow the procedure, you will receive an F in the course, which may affect your financial aid and/or VA educational benefits. Academic Integrity Texas A&M University -Central Texas values the integrity of the academic enterprise and strives for the highest standards of academic conduct. A&M-Central Texas expects its students, faculty, and staff to support the adherence to high standards of personal and scholarly conduct to preserve the honor and integrity of the creative community. Academic integrity is defined as a commitment to honesty, trust, fairness, respect, and responsibility. Any deviation by students from this expectation may result in a failing grade for the assignment and potentially a failing grade for the course. Academic misconduct is any act that improperly affects a true and honest evaluation of a student’s academic performance and includes, but is not limited to, cheating on an examination or other academic work, plagiarism and improper citation of sources, using another student’s work, collusion, and the abuse of resource materials. All academic misconduct concerns will be reported to the university’s Office of Student Conduct. Ignorance
of the university’s standards and expectations is never an excuse to act with a lack of integrity. When in doubt on collaboration, citation, or any issue, please contact your instructor before taking a course of action. For more information regarding the Student Conduct process, [https://www.tamuct.edu/student-affairs/student-conduct.html]. If you know of potential honor violations by other students, you may submit a report, [https://cm.maxient.com/reportingform.php?TAMUCentralTexas&layout_id=0]. Academic Accommodations At Texas A&M University-Central Texas, we value an inclusive learning environment where every student has an equal chance to succeed and has the right to a barrier-free education. The Office of Access and Inclusion is responsible for ensuring that students with a disability receive equal access to the university’s programs, services and activities. If you believe you have a disability requiring reasonable accommodations please contact the Office of Access and Inclusion, WH-212; or call (254) 501-5836. Any information you provide is private and confidential and will be treated as such. For more information please visit our Access & Inclusion Canvas page (log-in required) [https://tamuct.instructure.com/courses/717] Important information for Pregnant and/or Parenting Students Texas A&M University-Central Texas supports students who are pregnant and/or parenting. In accordance with requirements of Title IX and related guidance from US Department of Education’s Office of Civil Rights, the Dean of Student Affairs’ Office can assist students who are pregnant and/or parenting in seeking accommodations related to pregnancy and/or parenting. Students should seek out assistance as early in the pregnancy as possible. For more information, please visit Student Affairs [https://www.tamuct.edu/student-affairs/index.html]. Students may also contact the institution’s Title IX Coordinator. If you would like to read more about these requirements and guidelines online, please visit the website [http://www2.ed.gov/about/offices/list/ocr/docs/pregnancy.pdf]. Title IX of the Education Amendments Act of 1972 prohibits discrimination on the basis of sex and gender–including pregnancy, parenting, and all related conditions. A&M-Central Texas is able to provide flexible and individualized reasonable accommodation to pregnant and parenting students. All pregnant and parenting students should contact the Associate Dean in the Division of Student Affairs at (254) 501-5909 to seek out assistance. Students may also contact the University’s Title IX Coordinator. Tutoring Tutoring is available to all A&M-Central Texas students, both on-campus and online.
Subjects tutored on campus include Accounting, Advanced Math, Biology, Finance,
Statistics, Mathematics, and Study Skills. Tutors are available at the Tutoring Center in Warrior
Chat live with a tutor 24/7 for almost any subject from on your computer! Tutor.com is
an online tutoring platform that enables A&M-Central Texas students to log in and receive
online tutoring support at no additional cost. This tool provides tutoring in over 40 subject
areas. Access Tutor.com through Canvas.
University Writing Center Located in Warrior Hall 416, the University Writing Center (UWC) at Texas A&M University–Central Texas (TAMUCT) is a free workspace open to all TAMUCT students from 10:00 a.m.-5:00 p.m. Monday thru Thursday with satellite hours in the University Library Monday thru Thursday from 6:00-9:00 p.m. This semester, the UWC is also offering online only hours from 12:00-3:00 p.m. on Saturdays.
Tutors are prepared to help writers of all levels and abilities at any stage of the writing process. While tutors will not write, edit, or grade papers, they will assist students in developing more effective composing practices. By providing a practice audience for students’ ideas and writing, our tutors highlight the ways in which they read and interpret students’ texts, offering guidance and support throughout the various stages of the writing process. In addition, students may work independently in the UWC by checking out a laptop that runs the Microsoft Office suite and connects to WIFI, or by consulting our resources on writing, including all of the relevant style guides. Whether you need help brainstorming ideas, organizing an essay, proofreading, understanding proper citation practices, or just want a quiet place to work, the UWC is here to help!
Students may arrange a one-to-one session with a trained and experienced writing tutor by visiting the UWC during normal operating hours (both half-hour and hour sessions are available) or by making an appointment via WCOnline [https://tamuct.mywconline.com/]. In addition, you can email Dr. Bruce Bowles Jr. at [email protected] if you have any questions about the UWC and/or need any assistance with scheduling.
University Library The University Library provides many services in support of research across campus and at a distance. We offer over 200 electronic databases containing approximately 250,000 eBooks and 82,000 journals, in addition to the 85,000 items in our print collection, which can be mailed to students who live more than 50 miles from campus. Research guides for each subject taught at A&M-Central Texas are available through our website to help students navigate these resources. On campus, the library offers technology including cameras, laptops, microphones,
webcams, and digital sound recorders. Research assistance from a librarian is also available 24 hours a day through our online chat service, and at the reference desk when the library is open. Research sessions can be scheduled for more comprehensive assistance, and may take place on Skype or in-person at the library. Assistance may cover many topics, including how to find articles in peer-reviewed journals, how to cite resources, and how to piece together research for written assignments. Our 27,000-square-foot facility on the A&M-Central Texas main campus includes student lounges, private study rooms, group work spaces, computer labs, family areas suitable for all ages, and many other features. Services such as interlibrary loan, TexShare, binding, and laminating are available. The library frequently offers workshops, tours, readings, and other events. For more information, please visit our Library website [http://tamuct.libguides.com/index].
OPTIONAL POLICY STATEMENTS
A Note about Sexual Violence at A&M-Central Texas Sexual violence is a serious safety, social justice, and public health issue. The university offers support for anyone struggling with these issues. University faculty are mandated reporters, so if someone discloses that they were sexually assaulted (or a victim of Domestic/Dating Violence or Stalking) while a student at TAMUCT, faculty members are required to inform the Title IX Office. If you want to discuss any of these issues confidentially, you can do so through Student Counseling (254-501-5955) located on the second floor of Warrior Hall (207L). Sexual violence can occur on our campus because predators often feel emboldened, and victims often feel silenced or shamed. It is incumbent on ALL of us to find ways to actively create environments that tell predators we don’t agree with their behaviors and tell survivors we will support them. Your actions matter. Don’t be a bystander; be an agent of change. For additional information on campus policy and resources visit the Title IX webpage [https://www.tamuct.edu/departments/compliance/titleix.php]. Behavioral Intervention Texas A&M University-Central Texas cares about the safety, health, and well-being of its students, faculty, staff, and community. If you are aware of individuals for whom you have a concern, who are exhibiting behaviors that pose a threat to safety, or individuals causing a significant disruption to our community, please make a referral to the Behavioral Intervention Team. You can complete the referral online [https://cm.maxient.com/reportingform.php?TAMUCentralTexas&layout_id=2]. Anonymous referrals are accepted. Please see the Behavioral Intervention Team website for more information [https://www.tamuct.edu/student-affairs/bat.html]. If a person’s behavior poses an imminent threat to you or another, contact 911 or A&M-Central Texas University
1. There will be no bathroom breaks allowed during any exam. Be sure that you address this issue before beginning an exam.
2. Any student needing to take an exam at a different time as rest of students due to sickness or other accommodations will receive a different version of exam. This includes sickness, special accommodations, etc.…
3. All students needing special accommodations must submit an accommodation form from the Office of Access and Inclusion listing the specific accommodations needed. Students are responsible for scheduling their own exam times with the TAMUCT Testing Center.
4. Any student missing an exam in class for any other reason (i.e. illness, death in family, etc.…) must provide documentation for missing the exam (e.g. doctor’s note, obituary notice, etc.…). Exams must be made up within one week of original scheduled date, no exceptions.
Laboratory courses 1. Attendance policy: A maximum of 3 absences will be allowed; additional absences in
lab will result in an “F” for the entire course, regardless of excuse. 2. Laboratory Safety training: All students are required to take the mandatory Laboratory
Safety Training Module - found on in your Modules tab in CANVAS. You must take the training and bring the signed "Safety Agreement Form" to your instructor before you are allowed in lab!!! This is YOUR RESPONSIBILITY - any lab absences because you have not taken the training will be considered unexcused!
3. Laboratory Coats: Students who have laboratories in Warrior Hall (rms. 407, 410, 413) are required to purchase a laboratory coat from the TAMUCT Hanik Bookstore in Founder’s Hall. Due to the nature of chemicals used in Heritage Hall, lab coats will be provided for these laboratories.
INSTRUCTOR POLICIES. Read these carefully as I am strict with my policies.
Grading Policy and Point Breakdown. Grades in this course will be criteria-based on a
number of activities including exams, assignments, lab reports, and attendance. This means that
grades will not be curved and anyone achieving a 90% or above will receive an A in this course.
Grade Dispute Policy. Grading disputes must be put in writing (with justification such as
supporting statements from the text or another credible source) and given to me no earlier than
24 hours after the assignment has been returned. I will consider your request carefully, but
reserve the right to adjust your grade up or down.
Late Assignments. I expect all assignments to be turned in on time. Late assignments
interfere with my ability to provide timely, detailed feedback, as well as with your ability to learn
and process new material. Accordingly, any unauthorized late assignment will receive a 5%
reduction in grade for each day it is late. No assignments will be accepted after it has been
graded and returned.
Exams. The exams will be a mixture of multiple choices and short answers, designed to
provoke reflection, critical thought, and application of knowledge. You will receive a list of
several samples or real exam questions ahead of time. You are encouraged to prepare for the
exam by reviewing reading materials, outlining a draft of a response, and discussing these
thoughts with your peers. You will then demonstrate your individual, integrated thoughts on the
topic in a closed-book exam during the class period.
Missed exams. If you know you will miss an exam, please contact me BEFORE the exam. I will
gladly give make-up exams if the student has an unavoidable reason for missing the exam (i.e.
death in the family, severe illness). Keep in mind that I will expect documentation of your
reason for missing the exam (e.g. doctor’s note, obituary notice). Exams must be made up within
a week of the original scheduled date, no exceptions regardless of excuse.
What I expect of you. To get the most out of this class, you are expected to conduct yourself
in a professional manner, which includes contributing to class discussions, being punctual, and
notifying me of absences in advance.
Class Attendance. I expect that you attend each class session and arrive on time. If an
unavoidable situation arises that prevents you from attending class, I expect that you also
promptly contact me to discuss the missed material and get the notes from a classmate. I will not
distribute my notes to students as they are often abbreviated and do not contain the detail needed
to sufficiently understand the material.
What you can expect of me. You can expect me to start and end class on time, be available
through office hours, e-mail, and by appointment, be responsive to student suggestions for course
improvement, answer questions to the fullest extent possible and/or direct you to appropriate
resources, return graded assignments and exams within a reasonable time frame, and treat you
with respect as future colleagues.
Discussion. The topics in this class encompass a diversity of issues that merit in-depth thought
and discussion. Since individuals will be expressing their opinions, I expect that will you respect
others’ contributions, as you would want them to do for you.
Credits and Workload expectations. For undergraduate courses, one credit is defined as
equivalent to an average of two hours of learning effort per week (over a full semester) necessary
for an average student to receive an average grade for the course. A student taking a four-credit
class that meets for four hours a week should expect to spend an additional eight hours a week
outside the classroom in order to earn an average grade.
Class Structure. Classes will involve a balance of active lecture and engaging learning activities. I believe that students learn the theories and concepts much better when they have an active role. I know that this may be new to some of you, but please keep an open mind and I know that you will get more out of this class because of it. Copyright Notice Students should assume that all course material is copyrighted by the respective author(s). Reproduction of course material is prohibited without consent by the author and/or course instructor. Violation of copyright is against the law and Texas A&M University-Central Texas’ Code of Academic Honesty. All alleged violations will be reported to the Office of Student Conduct.
Copyright. (2019) by (LINH PHAM) at Texas A&M University-Central Texas, (COLLEGE OF ARTS AND SCIENCES); 1001 Leadership Place, Killeen, TX 76549; 254-(519-8012);